Bacterial dynamics govern growth trajectories and choline-derived trimethylamine production

Dietary choline is converted by gut bacteria into trimethylamine (TMA), the precursor of trimethylamine-N-oxide (TMAO), a biomarker linked to cardiovascular disease. Circulating TMAO levels vary widely across individuals, yet the bacterial interactions and functional determinants of TMA output remain poorly understood. Here, we sought to assess bacterial dynamics that characterize growth and TMA production using defined monoculture and reciprocal supernatant-transfer assays containing 20 mM d9-choline with Bacteroides eggerthii, Limosilactobacillus reuteri, and Clostridium sporogenes. Across species, d9-choline did not broadly alter monoculture growth. L. reuteri and C. sporogenes exhibited greater growth in B. eggerthii supernatant with d9-choline than without, whereas B. eggerthii in supernatant from the other species showed no change. Exposure to B. eggerthii supernatant modulated d9-TMA output in L. reuteri and C. sporogenes to different extents, indicating species-specific metabolic capacity. Notably, B. eggerthii produced detectable d9-TMA levels in supernatant from L. reuteri and C. sporogenes, despite lacking canonical TMA-producing genes, highlighting functional complexity beyond gene presence alone. Random forest identified growth and d9-TMA concentration as the discriminative features across conditions, and principal component analysis demonstrated that B. eggerthii supernatant shifted C. sporogenes toward the profiles of the other treatment groups. As a proof-of-concept, least squares regression of a generalized Lotka-Volterra model approximated selected microbial dynamics and yielded estimates of pairwise interaction coefficients. In conclusion, species-specific and inter-species signatures govern growth and choline-to-TMA conversion, reflecting the modulatory capacity of bacterial interactions. Our study provides a foundation for extending these insights into more complex communities and in vivo models relevant to TMAO-associated disease risk.